Mechanisms and regulation of human mitochondrial transcription.

The expression of mitochondrial genes is regulated in response to the metabolic needs of different cell types, but the basic mechanisms underlying this process are still poorly understood. In this Review, we describe how different layers of regulation cooperate to fine tune initiation of both mitochondrial DNA (mtDNA) transcription and replication in human cells. We discuss our current understanding of the molecular mechanisms that drive and regulate transcription initiation from mtDNA promoters, and how the packaging of mtDNA into nucleoids can control the number of mtDNA molecules available for both transcription and replication. Indeed, a unique aspect of the mitochondrial transcription machinery is that it is coupled to mtDNA replication, such that mitochondrial RNA polymerase is additionally required for primer synthesis at mtDNA origins of replication. We discuss how the choice between replication-primer formation and genome-length RNA synthesis is controlled at the main origin of replication (OriH) and how the recent discovery of an additional mitochondrial promoter (LSP2) in humans may change this long-standing model.

Treatment of a ruptured shallow trilobed cerebral aneurysm with the novel saccular endovascular aneurysm lattice (SEAL) device: A case report with one year follow-up.

Intrasaccular flow disruption is a viable alternative to other endovascular treatments for saccular or wide-necked bifurcation intracranial aneurysms; however, wide neck aneurysms with irregular shapes or shallow depth may not be amenable to treatment currently available intrasaccular devices. Here, we present the first ever case report of the novel Saccular Endovascular Aneurysm Lattice Embolization System (SEAL™). The versatile utility of the SEAL™ device is demonstrated in a patient with acute subarachnoid hemorrhage (SAH) from a ruptured, complex, left middle cerebral artery (MCA) trilobed shallow wide-necked bifurcation aneurysm. Deployment and implantation of the SEAL device were technically feasible, safe, and conformed well to the irregular shape of the complex, ruptured aneurysm. Immediate total aneurysm occlusion was observed after implantation. Importantly, 1-year angiographic follow-up demonstrated durable, complete occlusion with no safety concerns. The SEAL device is a promising new novel technology which has the potential to treat very shallow aneurysms with limited height and irregular, multilobulated aneurysms.

Development and testing of a multi-lingual Natural Language Processing-based deep learning system in 10 languages for COVID-19 pandemic crisis: A multi-center study.

Purpose: The COVID-19 pandemic has drastically disrupted global healthcare systems. With the higher demand for healthcare and misinformation related to COVID-19, there is a need to explore alternative models to improve communication. Artificial Intelligence (AI) and Natural Language Processing (NLP) have emerged as promising solutions to improve healthcare delivery. Chatbots could fill a pivotal role in the dissemination and easy accessibility of accurate information in a pandemic. In this study, we developed a multi-lingual NLP-based AI chatbot, DR-COVID, which responds accurately to open-ended, COVID-19 related questions. This was used to facilitate pandemic education and healthcare delivery. Methods: First, we developed DR-COVID with an ensemble NLP model on the Telegram platform (https://t.me/drcovid_nlp_chatbot). Second, we evaluated various performance metrics. Third, we evaluated multi-lingual text-to-text translation to Chinese, Malay, Tamil, Filipino, Thai, Japanese, French, Spanish, and Portuguese. We utilized 2,728 training questions and 821 test questions in English. Primary outcome measurements were (A) overall and top 3 accuracies; (B) Area Under the Curve (AUC), precision, recall, and F1 score. Overall accuracy referred to a correct response for the top answer, whereas top 3 accuracy referred to an appropriate response for any one answer amongst the top 3 answers. AUC and its relevant matrices were obtained from the Receiver Operation Characteristics (ROC) curve. Secondary outcomes were (A) multi-lingual accuracy; (B) comparison to enterprise-grade chatbot systems. The sharing of training and testing datasets on an open-source platform will also contribute to existing data. Results: Our NLP model, utilizing the ensemble architecture, achieved overall and top 3 accuracies of 0.838 [95% confidence interval (CI): 0.826-0.851] and 0.922 [95% CI: 0.913-0.932] respectively. For overall and top 3 results, AUC scores of 0.917 [95% CI: 0.911-0.925] and 0.960 [95% CI: 0.955-0.964] were achieved respectively. We achieved multi-linguicism with nine non-English languages, with Portuguese performing the best overall at 0.900. Lastly, DR-COVID generated answers more accurately and quickly than other chatbots, within 1.12-2.15 s across three devices tested. Conclusion: DR-COVID is a clinically effective NLP-based conversational AI chatbot, and a promising solution for healthcare delivery in the pandemic era.

Early Triple-Negative Breast Cancers in a Singapore Cohort Exhibit High PIK3CA Mutation Rates Associated With Low PD-L1 Expression.

Mutations in the PI3K pathway, particularly PIK3CA, were reported to be intimately associated with triple-negative breast cancer (TNBC) progression and the development of treatment resistance. We profiled PIK3CA and other genes on 166 early-stage TNBC tumors from Singapore for comparison to publicly available TNBC cohorts. These tumors were profiled transcriptionally using a NanoString panel of immune genes and multiplex immunohistochemistry, then manually scored for PD-L1-positivity using 2 clinically relevant clones, SP142 and 22C3. We discovered a higher rate of PIK3CA mutations in our TNBC cohort than in non-Asian cohorts, along with TP53, BRCA1, PTPN11, and MAP3K1 alterations. PIK3CA mutations did not affect overall or recurrence-free survival, and when compared with PIK3CAWT tumors, there were no differences in immune infiltration. Using 2 clinically approved antibodies, PIK3CAmut tumors were associated with PD-L1 negativity. Analysis of comutation frequencies further revealed that PIK3CA mutations tended to be accompanied by MAP kinase pathway mutation. The mechanism and impact of PIK3CA alterations on the TNBC tumor immune microenvironment and PD-L1 positivity warrant further study.

Physical Activity During Lockdowns Associated with the COVID-19 Pandemic: A Systematic Review and Multilevel Meta-analysis of 173 Studies with 320,636 Participants.

BACKGROUND: Many countries have restricted public life in order to contain the spread of the novel coronavirus (SARS-CoV2). As a side effect of related measures, physical activity (PA) levels may have decreased. OBJECTIVE: We aimed (1) to quantify changes in PA and (2) to identify variables potentially predicting PA reductions. METHODS: A systematic review with random-effects multilevel meta-analysis was performed, pooling the standardized mean differences in PA measures before and during public life restrictions. RESULTS: A total of 173 trials with moderate methodological quality (modified Downs and Black checklist) were identified. Compared to pre-pandemic, total PA (SMD - 0.65, 95% CI - 1.10 to - 0.21) and walking (SMD - 0.52, 95% CI - 0.29 to - 0.76) decreased while sedentary behavior increased (SMD 0.91, 95% CI: 0.17 to 1.65). Reductions in PA affected all intensities (light: SMD - 0.35, 95% CI - 0.09 to - 0.61, p = .013; moderate: SMD - 0.33, 95% CI - 0.02 to - 0.6; vigorous: SMD - 0.33, - 0.08 to - 0.58, 95% CI - 0.08 to - 0.58) to a similar degree. Moderator analyses revealed no influence of variables such as sex, age, body mass index, or health status. However, the only continent without a PA reduction was Australia and cross-sectional trials yielded higher effect sizes (p < .05). CONCLUSION: Public life restrictions associated with the COVID-19 pandemic resulted in moderate reductions in PA levels and large increases in sedentary behavior. Health professionals and policy makers should therefore join forces to develop strategies counteracting the adverse effects of inactivity.

Healthcare workers' self-regulatory eating behaviours are associated with being stress-free during the Covid-19 lockdown in Singapore.

Our study sought to examine the impact of the pandemic and the Circuit-breaker (CB) measures on dietary behaviours of healthcare workers (HCW). In addition, the association between self-regulatory eating behaviours and psychological stress was explored. Our study employed a cross-sectional anonymous survey that examined the demographics, dietary habits, self-regulatory eating behaviours (SR) and their association to stress levels of healthcare workers (HCWs) before and during the Circuit Breaker (CB) in Singapore. The survey was conducted over four weeks from May 17 to June 18, 2020. Snowball sampling was performed in the final week. A total of 707 participants took part in the survey. Due to the CB measures and modifications of work scope and work areas, there were significant changes in their dietary behaviors before CB versus during the CB period (n = 707), with many reducing the intake of vegetables (p = 0.018) while increasing their intake of unhealthy food choices such as canned drinks (p = 0.002), convenience food (p ≤ 0.001) and alcoholic drinks (p = 0.034). Before the CB period, 91.8% (602/656) of participants who intended to have a healthy diet were classified in medium-to-high SR groups whereas during the CB period, 87.7% (575/656) were in medium-to-high SR groups and the difference was statistically significant (p = 0.011). Nurses, administrative staff, HCWs of Chinese and Indian ethnicities, staff who did not complete university education and those who did not have domestic helpers were more likely to have reduced SR. Importantly, amongst participants who intended to have a healthy diet, 70.9% displayed no change or improved eating habits and showed medium-to-high levels of SR during CB. Participants with no changes in SR were 2.11 times more likely to be stress-free as compared to those who had deteriorated SR (OR 2.11 95% CI 1.27-3.48, p = 0.004). Due to CB measures and work modifications, dietary behaviours of HCWs deteriorated with increased intake of unhealthy food choices. HCWs who maintain their self-regulatory eating behaviour are more likely to be stress-free. Short screening questionnaires based on SR changes should be developed and explored as surveillance tools for assessment of HCWs' general well-being such that personalized interventions to vulnerable groups of workers could be implemented effectively on the ground.

Case report: Understanding the impact of persistent tissue-localization of SARS-CoV-2 on immune response activity via spatial transcriptomic analysis of two cancer patients with COVID-19 co-morbidity.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected half a billion people, including vulnerable populations such as cancer patients. While increasing evidence supports the persistence of SARS-CoV-2 months after a negative nasopharyngeal swab test, the effects on long-term immune memory and cancer treatment are unclear. In this report, we examined post-COVID-19 tissue-localized immune responses in a hepatocellular carcinoma (HCC) patient and a colorectal cancer (CRC) patient. Using spatial whole-transcriptomic analysis, we demonstrated spatial profiles consistent with a lymphocyte-associated SARS-CoV-2 response (based on two public COVID-19 gene sets) in the tumors and adjacent normal tissues, despite intra-tumor heterogeneity. The use of RNAscope and multiplex immunohistochemistry revealed that the spatial localization of B cells was significantly associated with lymphocyte-associated SARS-CoV-2 responses within the spatial transcriptomic (ST) niches showing the highest levels of virus. Furthermore, single-cell RNA sequencing data obtained from previous (CRC) or new (HCC) ex vivo stimulation experiments showed that patient-specific SARS-CoV-2 memory B cells were the main contributors to this positive association. Finally, we evaluated the spatial associations between SARS-CoV-2-induced immunological effects and immunotherapy-related anti-tumor immune responses. Immuno-predictive scores (IMPRES) revealed consistent positive spatial correlations between T cells/cytotoxic lymphocytes and the predicted immune checkpoint blockade (ICB) response, particularly in the HCC tissues. However, the positive spatial correlation between B cells and IMPRES score was restricted to the high-virus ST niche. In addition, tumor immune dysfunction and exclusion (TIDE) analysis revealed marked T cell dysfunction and inflammation, alongside low T cell exclusion and M2 tumor-associated macrophage infiltration. Our results provide in situ evidence of SARS-CoV-2-generated persistent immunological memory, which could not only provide tissue protection against reinfection but may also modulate the tumor microenvironment, favoring ICB responsiveness. As the number of cancer patients with COVID-19 comorbidity continues to rise, improved understanding of the long-term immune response induced by SARS-CoV-2 and its impact on cancer treatment is much needed.

The human mitochondrial genome contains a second light strand promoter.

The human mitochondrial genome must be replicated and expressed in a timely manner to maintain energy metabolism and supply cells with adequate levels of adenosine triphosphate. Central to this process is the idea that replication primers and gene products both arise via transcription from a single light strand promoter (LSP) such that primer formation can influence gene expression, with no consensus as to how this is regulated. Here, we report the discovery of a second light strand promoter (LSP2) in humans, with features characteristic of a bona fide mitochondrial promoter. We propose that the position of LSP2 on the mitochondrial genome allows replication and gene expression to be orchestrated from two distinct sites, which expands our long-held understanding of mitochondrial gene expression in humans.

Non-coding 7S RNA inhibits transcription via mitochondrial RNA polymerase dimerization.

The mitochondrial genome encodes 13 components of the oxidative phosphorylation system, and altered mitochondrial transcription drives various human pathologies. A polyadenylated, non-coding RNA molecule known as 7S RNA is transcribed from a region immediately downstream of the light strand promoter in mammalian cells, and its levels change rapidly in response to physiological conditions. Here, we report that 7S RNA has a regulatory function, as it controls levels of mitochondrial transcription both in vitro and in cultured human cells. Using cryo-EM, we show that POLRMT dimerization is induced by interactions with 7S RNA. The resulting POLRMT dimer interface sequesters domains necessary for promoter recognition and unwinding, thereby preventing transcription initiation. We propose that the non-coding 7S RNA molecule is a component of a negative feedback loop that regulates mitochondrial transcription in mammalian cells.

Consensus statement on Singapore integrated 24-hour activity guide for children and adolescents.

INTRODUCTION: Lifestyle activities, such as regular physical activity, are important for good metabolic health and the prevention of non-communicable diseases. Epidemiological studies highlight an increase in the proportion of overweight children in Singapore. A workgroup was formed to develop recommendations to encourage children and adolescents (aged 7-17 years) to adopt a holistic approach towards integrating beneficial activities within a daily 24-hour period for good metabolic and general health. METHODS: The Grading of Recommendations Assessment, Development and Evaluation (GRADE) Evidence to Decision framework was employed to formulate the public health question, assess the evidence and draw conclusions for the guide. The evidence for international 24-hour movement guidelines, and guidelines for physical activity, sedentary behaviour, and sleep and eating habits were reviewed. An update of the literature review from August 2018 to end of September 2020 was conducted through an electronic search of Medline and Cumulative Index to Nursing and Allied Health Literature (CINAHL) databases. RESULTS: Ten consensus statements were developed. The statements focused on the overall aim of achieving good metabolic health through integration of these activities and initiatives: light and moderate- to vigorous-intensity physical activity on a regular basis; muscle- and bone-strengthening activities; limiting sedentary behaviour; regular and adequate sleep; good eating habits and choosing nutritionally balanced foods and drinks; practise safety in exercise; and aiming to achieve more or all aforementioned recommendations for the best results. CONCLUSION: This set of recommendations provides guidance to encourage Singapore children and adolescents to adopt health-beneficial activities within a 24-hour period.

Barriers and facilitators to exercise among adult cancer survivors in Singapore.

PURPOSE: Exercise can help cancer survivors manage sequela, treatment side effects, improve overall quality of life, and is recommended for most. The purpose of this study was to investigate exercise behavior and factors influencing exercise engagement among cancer survivors at the National Cancer Centre, Singapore (NCCS). METHODS: This cross-sectional study was inclusive of survivors of all cancer types and stages who were at least 21 years of age and had undergone chemotherapy at the NCCS. Surveys were utilized to assess survivor barriers and facilitators to exercise and to retrospectively assess physical activity and exercise behaviors at 4 cancer-related time periods (pre-diagnosis and post-diagnosis before, during, or after chemotherapy). RESULTS: A total of 102 cancer survivors were enrolled; 60% were diagnosed with stage IV cancer. Predominant cancer types included lower gastrointestinal tract (25.5%) and breast cancer (21.6%). Prior to cancer diagnosis, 90.2% of participants reported aerobic activity satisfying NCCN guidelines. Significant reductions in reported exercise, and physical activity, were observed following cancer diagnosis that persisted during chemotherapy. Key exercise facilitators included the desire to remain healthy (86.3%) and to improve sleep and mental well-being (73.5%). Key barriers included side effects of treatment (52.0%). Only 46.1% of survivors reported receiving exercise guidance from healthcare professionals following diagnosis. CONCLUSION: Overall, even among this notably active cohort of Singaporean survivors, opportunities for increased exercise engagement throughout the survivorship continuum remain. Increased education regarding the benefits of exercise to survivors as well as guidance regarding exercise modalities including resistance training is greatly needed as well.

Physical activity levels and mental health burden of healthcare workers during COVID-19 lockdown.

The outbreak of COVID-19 has precipitated international lockdown measures to curb disease transmissions. The closure of public activity spaces as well as changes in pandemic workload may disrupt healthcare workers' physical activity and self-care routines. We sought to examine the association between physical activity levels and mental health burden of healthcare workers during the COVID-19 lockdown in Singapore. This cross-sectional study comprised of an multidomain survey that was administered digitally to 707 healthcare workers between 17 May and 18 June 2020. Exercise frequency, duration and intensity of these healthcare workers had reduced significantly during the lockdown compared to pre-lockdown. 25.3%, 37.2%, and 11.9% had screened positive for moderate-to-extremely-severe depression, anxiety and stress respectively. Reductions in exercise duration was a significant risk factor for mild stress and moderate-to-severe depression while increase in exercise frequency was found to be a protective factor against depressed mood. Our study revealed that a short-term reduction in physical activity levels during lockdown was associated with poorer psychological outcomes. Given the protection that exercise confers on depression, physical activity should be promoted at the workplace and at home to support healthcare workers to cope through this protracted health crisis.

Asian Pacific Society of Cardiology Consensus Recommendations for Pre-participation Screening in Young Competitive Athletes.

Sports-related sudden cardiac death is a rare but devastating consequence of sports participation. Certain pathologies underlying sports-related sudden cardiac death could have been picked up pre-participation and the affected athletes advised on appropriate preventive measures and/or suitability for training or competition. However, mass screening efforts - especially in healthy young populations - are fraught with challenges, most notably the need to balance scarce medical resources and sustainability of such screening programmes, in healthcare systems that are already stretched. Given the rising trend of young sports participants across the Asia-Pacific region, the working group of the Asian Pacific Society of Cardiology (APSC) developed a sports classification system that incorporates dynamic and static components of various sports, with deliberate integration of sports events unique to the Asia-Pacific region. The APSC expert panel reviewed and appraised using the Grading of Recommendations Assessment, Development, and Evaluation system. Consensus recommendations were developed, which were then put to an online vote. Consensus was reached when 80% of votes for a recommendation were agree or neutral. The resulting statements described here provide guidance on the need for cardiovascular pre-participation screening for young competitive athletes based on the intensity of sports they engage in.

Factors to Consider in the Use of Vital Signs Wearables to Minimize Contact With Stable COVID-19 Patients: Experience of Its Implementation During the Pandemic.

The COVID-19 pandemic has created a huge burden on the healthcare industry worldwide. Pressures to increase the isolation healthcare facility to cope with the growing number of patients led to an exploration of the use of wearables for vital signs monitoring among stable COVID-19 patients. Vital signs wearables were chosen for use in our facility with the purpose of reducing patient contact and preserving personal protective equipment. The process of deciding on the wearable solution as well as the implementation of the solution brought much insight to the team. This paper presents an overview of factors to consider in implementing a vital signs wearable solution. This includes considerations before deciding on whether or not to use a wearable device, followed by key criteria of the solution to assess. With the use of wearables rising in popularity, this serves as a guide for others who may want to implement it in their institutions.

Leveraging advances in immunopathology and artificial intelligence to analyze in vitro tumor models in composition and space.

Cancer is the leading cause of death worldwide. Unfortunately, efforts to understand this disease are confounded by the complex, heterogenous tumor microenvironment (TME). Better understanding of the TME could lead to novel diagnostic, prognostic, and therapeutic discoveries. One way to achieve this involves in vitro tumor models that recapitulate the in vivo TME composition and spatial arrangement. Here, we review the potential of harnessing in vitro tumor models and artificial intelligence to delineate the TME. This includes (i) identification of novel features, (ii) investigation of higher-order relationships, and (iii) analysis and interpretation of multiomics data in a (iv) holistic, objective, reproducible, and efficient manner, which surpasses previous methods of TME analysis. We also discuss limitations of this approach, namely inadequate datasets, indeterminate biological correlations, ethical concerns, and logistical constraints; finally, we speculate on future avenues of research that could overcome these limitations, ultimately translating to improved clinical outcomes.

Drastic Reductions in Mental Well-Being Observed Globally During the COVID-19 Pandemic: Results From the ASAP Survey.

Most countries affected by the COVID-19 pandemic have repeatedly restricted public life to control the contagion. However, the health impact of confinement measures is hitherto unclear. We performed a multinational survey investigating changes in mental and physical well-being (MWB/PWB) during the first wave of the pandemic. A total of 14,975 individuals from 14 countries provided valid responses. Compared to pre-restrictions, MWB, as measured by the WHO-5 questionnaire, decreased considerably during restrictions (68.1 ± 16.9 to 51.9 ± 21.0 points). Whereas 14.2% of the participants met the cutoff for depression screening pre-restrictions, this share tripled to 45.2% during restrictions. Factors associated with clinically relevant decreases in MWB were female sex (odds ratio/OR = 1.20, 95% CI: 1.11-1.29), high physical activity levels pre-restrictions (OR = 1.29, 95% CI 1.16-1.42), decreased vigorous physical activity during restrictions (OR = 1.14, 95% CI: 1.05-1.23), and working (partially) outside the home vs. working remotely (OR = 1.29, 95% CI: 1.16-1.44/OR = 1.35, 95% CI: 1.23-1.47). Reductions, although smaller, were also seen for PWB. Scores in the SF-36 bodily pain subscale decreased from 85.8 ± 18.7% pre-restrictions to 81.3 ± 21.9% during restrictions. Clinically relevant decrements of PWB were associated with female sex (OR = 1.62, 95% CI: 1.50-1.75), high levels of public life restrictions (OR = 1.26, 95% CI: 1.18-1.36), and young age (OR = 1.10, 95% CI: 1.03-1.19). Study findings suggest lockdowns instituted during the COVID-19 pandemic may have had substantial adverse public health effects. The development of interventions mitigating losses in MWB and PWB is, thus, paramount when preparing for forthcoming waves of COVID-19 or future public life restrictions.

A Pandemic within the Pandemic? Physical Activity Levels Substantially Decreased in Countries Affected by COVID-19.

Governments have restricted public life during the COVID-19 pandemic, inter alia closing sports facilities and gyms. As regular exercise is essential for health, this study examined the effect of pandemic-related confinements on physical activity (PA) levels. A multinational survey was performed in 14 countries. Times spent in moderate-to-vigorous physical activity (MVPA) as well as in vigorous physical activity only (VPA) were assessed using the Nordic Physical Activity Questionnaire (short form). Data were obtained for leisure and occupational PA pre- and during restrictions. Compliance with PA guidelines was calculated based on the recommendations of the World Health Organization (WHO). In total, n = 13,503 respondents (39 ± 15 years, 59% females) were surveyed. Compared to pre-restrictions, overall self-reported PA declined by 41% (MVPA) and 42.2% (VPA). Reductions were higher for occupational vs. leisure time, young and old vs. middle-aged persons, previously more active vs. less active individuals, but similar between men and women. Compared to pre-pandemic, compliance with WHO guidelines decreased from 80.9% (95% CI: 80.3-81.7) to 62.5% (95% CI: 61.6-63.3). Results suggest PA levels have substantially decreased globally during the COVID-19 pandemic. Key stakeholders should consider strategies to mitigate loss in PA in order to preserve health during the pandemic.

An Optimized Protocol for Proximity Biotinylation in Confluent Epithelial Cell Cultures Using the Peroxidase APEX2.

The peroxidase APEX2 has been used widely for proximity biotinylation and subsequent proteomics analyses. However, the poor membrane permeability of the biotin phenol substrate and the inhibitory effect of peroxide on the enzyme's activity has hampered proximity labeling in certain cell culture systems and tissues. Here, we describe an APEX2 protocol that uses alternative peroxide and biotin phenol concentrations. The protocol permits robust proximity biotinylation in confluent epithelial cell cultures and may be applicable to other cell cultures and tissues. For complete details on the use and execution of this protocol, please refer to Tan et al. (2020).